Protocol for optical clearing and imaging of fluorescently labeled ex vivo rat brain slices

Abstract

Tissue clearing is commonly used for whole-brain imaging but seldom used for brain slices. Here, we present a simple protocol to slice, immunostain, and clear sections of adult rat brains for subsequent high-resolution confocal imaging. The protocol does not require toxic reagents or specialized equipment. We also provide instructions for culturing of rat brain slices free floating on permeable culture inserts, maintained in regular CO₂ incubators, and handled only at media change.

Keywords: Cell Biology; Cell culture; Microscopy; Model Organisms; Neuroscience.